I spent Sunday morning wandering in and out of the ‘Tools and Resources from EBI’ session here at PAG. Some EBI resources for plant science will be very familiar to some of our community, but the presenters gave accessible talks that included some news and advice, so I thought I’d round them up for you.

Maria Keays presented ArrayExpress and ExpressionAtlas. These are the functional genomics tools from EBI. Keays defined functional genomics as the study of gene expression, gene function and gene regulation – these tools certainly aren’t just for microarray data!

Users submit their data to ArrayExpress via the Annotare submission tool, which encourages inclusion of information about how the samples were grown all the way through to data generation. Keays acknowledged that a user may encounter an error message they can’t get around, and assured us that emails sent to the helpdesk (Arrayexpress@ebi.ac.uk) are responded to quickly. Once submitted, the dataset and associated metadata is checked by a human curator before the user can upload it. The data can stay private until publication because two logins are provided; one for the submitter and one for the reviewer of the paper they hope to publish.

We’ve been encouraging our community to share data on NCBI GEO because it is able to disseminate almost any data type. But for functional genomics data, ArrayExpress is just as acceptable to journals as GEO, and the Annotare submission tool requires more extensive metadata and more stringent standards than GEO. (more…)

Just a quick blog post this week on some new plant science podcasts, for your entertainment!

First, Radio 4’s much-retweeted Plants: From Roots to Riches. This programme has been running all month and ends today so it’s not really news, but I’ve been listening to this bit by bit and was delighted to hear a familiar voice in the ‘Signals of Growth‘ episode. Nick Harberd, one of our Advisory Committee members, discussed the Green Revolution wheat and rice varieties with presenter Kathy Willis.

This is a great series, although the episodes are quite short and only focus on a small area of plant science so I’d advise skipping any episodes on a topic you know too much about or that just isn’t of interest to you. Highlights for me so far have been the ‘Blight on the Landscape‘ episode about plant-microbe interactions, which had a very interesting section on Beatrix Potter’s work on lichens; and the episode based entirely around Kew’s Arboretum, ‘An Ill Wind‘, which gave me a new appreciation of the great value of tree science and forestry.

Second, videos of talks from the UK Plant Sciences Federation conference PlantSci 2014 are now available on the Journal of Experimental Botany YouTube channel. The talks were all excellent and the videos make good teaching resources. All the speakers pitched their science for a well-informed general audience, and all were clear about why their research is important. The highlight of the conference for me was the panel discussion about UK plant science challenges, achievements and future needs and I’m happy to see that it’s there in it’s entirety, including the comments from the floor – all 1 hour 27 minutes of it.

It’s been very quiet here on the blog recently, but we’re pretty much caught up after being away at the International Conference on Arabidopsis Research in Vancouver (you can still see the #ICAR2014 stream here). Things will be back to normal very soon.

Last week I was in Helsinki for a plant synthetic biology meeting, and I learned a lot about existing European synbio tools, resources and research. There’s a short Storify of Tweets from the meeting here, and I’ll do a round-up post very soon. But today I’m highlighting a tool presented at the workshop, which was also presented at our SynBio workshop last year andat PlantSci 2014 but still hasn’t really featured on this blog (rather remiss of me, I know).

The Golden Gate cloning and related MoClo systems were presented (PDF) by one of its inventors, Sylvestre Marillonnet, at our synbio workshop last year. Sylvestre has worked with Nicola Patron, Head of Synthetic Biology at The Sainsbury Laboratory, to make a MoClo toolkit and set of parts available on Addgene. The toolkit includes 39 parts encoding promoters and 5′ untranslated regions; antigenic tags; sub-cellular localisation signals; reporter genes; selectable marker genes; terminators; 3′ untranslated regions; a suppressor of silencing; and two linkers.

Unfortunately the paper describing the toolkit is behind a paywall, but I’ve been tipped off as to where to find all the practical information you need:

1. The supplementary data is accessible to anyone, and it is very informative. SD 2 and 4 list modules in the toolkit and parts kit respectively.

Tamas Dalmay, Professor of RNA Biology at the University of East Anglia (Norwich), has developed a robust, simple method of profiling small RNAs using next generation sequencing. Here he explains his novel HD adapters and why they are more reliable than existing commercial adapters.

Figure 1c from Sorefan et al., 2012: The structure of miR-29b with the Illumina adapters (top) and some of the structures formed by HD adapters (bottom).

Small RNAs (sRNAs) are key regulators of gene expression, and accurate representation of sRNA in sequencing experiments is critical to the interpretation of biological data. Next generation sequencing (NGS) is now the gold standard for profiling and discovering new sRNAs, so it is essential that the tools and protocols used in NGS generate accurate, reliable sequence data.

RNA ligases are essential in creating cDNA libraries prior to NGS sequencing. However, a number of recent publications reported that RNA ligases used in cDNA preparation actually mediate sequence specific ligation, so NGS approaches using these RNA ligases do not represent all sRNA present in biological samples. These publications highlighted the limitations associated with RNA ligases, questioning the reliability of currently widely used NGS approaches and the data generated from them.

Sequence specific ligation occurs because the ligases preferentially ligate ends that are more likely to be close to each other. This means that sRNAs that can efficiently anneal to the adapters have a higher chance of being ligated (Jayaprakash et al. 2011, Hafner et al. 2011 and Sorefan et al. 2012).

While identifying that cloning bias in sRNA libraries is RNA ligase dependent, our group at the School of Biological Sciences, University of East Anglia (Norwich), developed a novel, simple, robust solution to overcome this problem (Sorefan et al. 2012).

We developed a set of adapters (High Definition or HD adapters) that contain degenerated nucleotides, meaning they are a pool of many sequences instead of one fixed sequence. Consequently, many different sRNAs can form a stable duplex with them, leading to better coverage and more quantitative libraries. We have shown that using the HD adapters: (more…)

The GARNet team travelled up to York last week for the PlantSci 2014 conference. It was a fantastic event and I highly recommend it for future years. The variation between talks, which were all perfectly pitched for a general plant science audience, made the sessions exciting and maintained everyone’s interest.

A highlight of the conference was the Panel Discussion on the Future of UK Plant Science. The Panelists – Mike Bushell, Mark Chase, Sarah Gurr, Sandy Knapp and Dale Sanders – responded to the Status Report (download the PDF here) and spoke briefly about what they felt were the most important challenges for the UK plant science community to deal with.

To me, the most significant issues were put forward by early career researchers from the floor. The Panel and the report, which drew data from a community-wide survey, emphasised skills shortages and a lack of young talent entering the field; but several young researchers present spoke out about lack of support for those young scientists that are working in the field.

One person on a PhD program with funding for a short internship in industry or policy found it difficult to find a placement related to plant science. Two final year PhD students from very different research backgrounds spoke of their frustration in not knowing where to look for post-doctoral jobs. Despite being highly trained in areas within the ‘skills gap’ often referred to in reports, including the UKPSF report, they felt that academic post-doc positions (and the uncertain future that comes with them) were the only options they had.

If you feel passionately about education, training and/or plant science careers and career paths, see UKPSF working group call document (PDF) on information on what the UKPSF is doing to tackle these challenges. There will be UKPSF working groups on Training & Skills, Funding, Portfolio Balance, Regulation, and Translation.

Last week I was at ASPB’s annual conference, Plant Biology 2013. It was a great week and I learned a lot of new science and discovered a lot of new resources to share with UK plant scientists – some brand new, and some golden oldies that get better with time.

First of all through, some shameless self-promotion – I wrote a report for New Phytologist on the UK’s own Plant Science conference, PlantSci 2013, with Ruth and Mimi. It’s now published (open access) here.

For the last three years, ASPB have been working on a decadal vision for plant science in the US. The final report was released in July, and will be rolled out to Congress in the autumn with the aim of raising awareness of the importance of plant science and getting extra funding. You can download the report, entitled Unleashing a Decade of Innovation in Plant Science, here. The Plant Science Research Summit website also explains how the report was written and includes the preliminary report from 2011.

Kate Dreher gave an excellent talk in the Genomic Tools minisymposium on the ever expanding output from the Plant Metabolomic Network, the free online tool which enables users to find and predict genes or proteins, other metabolites, reactions, and pathways. In June this year seven new databases were released, including BarleyCyc and OryzaCyc. In July, many existing databases were updated – AraCyc 11.5 now contains data on 597 pathways, 9041 enzymes, 3490 interactions, and 2613 compounds. For tutorials, see this page. (more…)

Part of Figure 7 from Green et al., showing the an example of Phenophyte output.

At the end of last year, you may have missed two useful publications from Plant Methods which use new free online tools to make your life easier.

Phenophyte can help you measure 2D areas quickly and accurately. It was described in November’s Plant Methods by Green et al., a team mainly from Columbia, USA. Users chose if they want to analyse indivudial images, compare before/after images (as shown in the figure to the left), or analyse a timecourse. They then upload the images – the upload tool allows up to 2GB or 500 images, and sequential uploads are possible if required. The computational results can be previewed before submitting the job. When processing is complete, the user will be emailed a link to the results, which must be downloaded within a week. The manual provides detailed tips on how to take the photographs to upload, and the guidance is standard with the exception of the use of a colour/size checker (for example, this one), and the interface is straightforward and friendly.

A more specialized application is CalloseMeasurer, from the Robatzek group at The Sainsbury Laboratory. Zhou et al. describe a piece of software for quantifying callose deposition with enough accuracy to quantify the growth of filamentous pathogens within a plant by recognising the spreading network of callose deposition caused by the pathogen. The paper is heavy on technical detail, but guides readers through using CalloseMeasurer in the ‘Image Processing’ section of the paper. Users must have Acapella software installed, and they simply drag and drop the CalloseMeasurer script into the application window and start using the programme.

Warwick Crop Centre are holding an Open Afternoon on 19th September. Visitors will be able to view the facilities, including field and glasshouse trials, and learn about the research and training opportunities.

Also on 19th September, EBI are holding a training course for PhD students and post-docs to train them to use the new PhytoPath resource.

The BBSRC funded Wheat Improvement Strategic Programme are running a course on wheat genetics at the John Innes Centre on 19-22 November 2012. There are only 10 places available but it will be a good introduction to cereals research and crop breeding for undergraduates, postgraduates or junior breeders. Apply here until 1 October.

There will be an international meeting on Imaging in Cell Biology in Windsor Great Park on 14-17 October. There are free places for graduate students and post-docs.

This bumper GARNet Research Roundup begins with two sets of papers in related areas. First are three papers that investigate the biology of plasmodesmatata. These include work from the Faulkner lab at the JIC, the Band lab at Nottingham and a broad European collaboration that includes co-authors from Durham, Cambridge and St Andrews. The second[…]

Naresh Loudya from Royal Holloway University of London discusses a recent paper published in the Philosophical Transactions of the Royal Society B entitled ‘Retrograde signalling in a virescent mutant triggers an anterograde delay of chloroplast biogenesis that requires GUN1 and is essential for survival‘. Apologies for the high background noise early in the recording. http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/05/Loudya_200520_edita-19052020-12.25.mp3Podcast:[…]

This edition of GARNet Research Roundup begins with two studies from the John Innes Centre. The first takes a detailed look at meiosis in Arabidopsis arenosa and the second introduces a novel mode of auxin perception. The third paper from the Grierson lab in Bristol uses innovative methods to assess root-soil cohesion through study of[…]

Andre Kuhn works with Lars Ostergaard at the John Innes Centre and discusses a recent Elife paper entitled ‘Direct ETTIN-auxin interaction controls chromatin states in gynoecium development‘. We discuss a new paradigm for auxin perception in the control gene expression. http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/04/200420_Kuhn_edit-20042020-13.57.mp3Podcast: Play in new window | DownloadSubscribe: iTunes | Android | RSS

Bethany Eldridge and Tom Denbigh are co-first authors on a recent paper in Communications Biology entitled ‘Micro-scale interactions between Arabidopsis root hairs and soil particles influence soil erosion‘. We discuss the innovative experimental procedures that they designed to measure the interaction of root hairs with their environment! http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/04/2004254_Eldridge_edit-24042020-11.16.mp3Podcast: Play in new window | DownloadSubscribe: iTunes[…]

GARNet conducted a short survey to assess community-interest in an UK-focused webinar series that will highlights the excellence in UK plant science. Approximately 100 respondants were supportive of the idea so we are kicking off the GARNet-Presents Webinar series on May 5th 2020. This series owes a huge debt of thanks to the widely popular[…]

Chris Morgan who works at the John Innes Centre discusses a recent PNAS paper entitled ‘Derived alleles of two axis proteins affect meiotic traits in autotetraploid Arabidopsis arenosa‘. We discuss the technical challenges of this research as well as the difficulties working from home (or not) with a super-resolution microscope! http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/04/Morgan_200417_edit-17042020-14.59.mp3Podcast: Play in new window[…]

The use of automatic image analysis in the biological sciences has increased significantly in recent years, especially with automated image capture and the rise of phenotyping. This online course will help improve your understanding of image analysis methods, and improve your practical skills and ability to apply the techniques to your images. You will explore[…]

This Easter edition of the GARNet Research Roundup begins with research from Aberystwyth University that has developed a system for studying self-incompatability in self-compatible Arabidopsis. Next is an outstanding community-focussed study led from the John Innes Centre that outlines the development of new resources that better enable discovery-led science to be conducted within hexaploid wheat.[…]

Ludi Wang and Maurice Bosch work at Aberystwyth University and talk to the GARNet Community podcast about a recent paper in JXBot entitled ‘New opportunities and insights into Papaver self-incompatibility by imaging engineered Arabidopsis pollen‘. We discuss the challenges of live imaging Arabidopsis pollen tubes growing in liquid media!! http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/04/Bosch_Wang_200406_edit-07042020-08.56.mp3Podcast: Play in new window |[…]